SMTL ID : 6dur.1

Citrobacter freundii tyrosine phenol-lyase complexed with L-phenylalanine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-tetramer

Ligands

2 x P71: (2E)-2-{[(Z)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4(1H)-ylidene}methyl]imino}-3-phenylpropanoic acid(Non-covalent)

P71.1: 16 residues within 4Å: Chain A: T.48, Q.97, G.98, R.99, E.102, F.122, T.124, N.184, D.213, T.215, R.216, S.253, K.255, K.256, R.403 Chain B: Y.70 23 PLIP interactions: 22 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:F.122, A:T.215, B:Y.70 Hydrogen bonds: A:T.48, A:S.50, A:Q.97, A:G.98, A:R.99, A:T.125, A:N.184, A:D.213, A:R.216, A:R.216, A:S.253, A:S.253, A:K.256 Water bridges: A:K.255 Salt bridges: A:R.99, A:R.216, A:K.256, A:K.256, A:R.403 pi-Stacking: A:F.122 P71.7: 16 residues within 4Å: Chain C: T.48, Q.97, G.98, R.99, E.102, F.122, T.124, N.184, D.213, T.215, R.216, S.253, K.255, K.256, R.403 Chain D: Y.70 24 PLIP interactions: 22 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:F.122, C:T.215, D:Y.70 Hydrogen bonds: C:T.48, C:S.50, C:Q.97, C:G.98, C:R.99, C:N.184, C:D.213, C:R.216, C:R.216, C:S.253, C:S.253, C:K.256 Water bridges: C:E.102, C:K.255, D:Y.70 Salt bridges: C:R.99, C:R.216, C:K.256, C:K.256, C:R.403 pi-Stacking: C:F.122

4 x K: POTASSIUM ION(Non-covalent)

K.2: 3 residues within 4Å: Chain A: E.68 Chain B: G.51, N.261 5 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: B:G.51, B:N.261, A:E.68, H2O.4, H2O.15 K.3: 3 residues within 4Å: Chain A: G.51, N.261 Chain B: E.68 5 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: B:E.68, A:G.51, A:N.261, H2O.5, H2O.15 K.8: 3 residues within 4Å: Chain C: E.68 Chain D: G.51, N.261 5 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: D:G.51, D:N.261, C:E.68, H2O.27, H2O.38 K.9: 3 residues within 4Å: Chain C: G.51, N.261 Chain D: E.68 5 PLIP interactions: 2 interactions with chain C, 1 interactions with chain D, 2 Ligand-Water interactions Metal complexes: C:G.51, C:N.261, D:E.68, H2O.28, H2O.38

2 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.4: 3 residues within 4Å: Chain A: K.225, E.232, Y.311 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.225 Water bridges: A:Y.311, A:E.312 PGE.10: 3 residues within 4Å: Chain C: K.225, E.232, Y.311 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:K.225 Water bridges: C:Y.311, C:E.312

2 x P33: 3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL(Non-covalent)

P33.5: 11 residues within 4Å: Chain A: N.1, Y.2, P.3, Y.323, Y.413, A.414, D.417 Chain D: Y.2, Y.323, A.414, D.417 8 PLIP interactions: 6 interactions with chain A, 2 interactions with chain D Hydrogen bonds: A:N.1, A:Y.323, A:A.414, D:Y.323, D:D.417 Water bridges: A:Y.2, A:A.4, A:A.4 P33.11: 11 residues within 4Å: Chain B: Y.2, Y.323, A.414, D.417 Chain C: N.1, Y.2, P.3, Y.323, Y.413, A.414, D.417 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:N.1, C:A.414 Water bridges: C:Y.2, C:A.4, C:A.4

2 x P70: (E)-N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-L-phenylalanine(Covalent)

P70.6: 18 residues within 4Å: Chain A: Y.70 Chain B: T.48, S.50, Q.97, G.98, R.99, E.102, F.122, T.124, T.125, N.184, D.213, T.215, R.216, S.253, K.255, K.256, R.403 19 PLIP interactions: 1 interactions with chain A, 18 interactions with chain B Hydrophobic interactions: A:Y.70, B:F.122 Hydrogen bonds: B:Q.97, B:G.98, B:R.99, B:N.184, B:R.216, B:R.216, B:S.253, B:S.253 Water bridges: B:S.50, B:S.50 Salt bridges: B:R.99, B:R.216, B:K.255, B:K.256, B:K.256, B:R.403 pi-Stacking: B:F.122 P70.12: 18 residues within 4Å: Chain C: Y.70 Chain D: T.48, S.50, Q.97, G.98, R.99, E.102, F.122, T.124, T.125, N.184, D.213, T.215, R.216, S.253, K.255, K.256, R.403 22 PLIP interactions: 21 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:F.122, C:Y.70 Hydrogen bonds: D:T.48, D:Q.97, D:G.98, D:R.99, D:T.125, D:N.184, D:T.215, D:R.216, D:R.216, D:S.253, D:S.253 Water bridges: D:S.50, D:S.50 Salt bridges: D:R.99, D:R.216, D:K.255, D:K.256, D:K.256, D:R.403 pi-Stacking: D:F.122

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Phillips, R.S. et al., Crystal Structures of Wild-Type and F448A Mutant Citrobacter freundii Tyrosine Phenol-Lyase Complexed with a Substrate and Inhibitors: Implications for the Reaction Mechanism. Biochemistry (2018)

Release Date

2018-10-10

Peptides

Tyrosine phenol-lyase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Tyrosine phenol-lyase